SBGNview.data

Supporting datasets for SBGNview package


Bioconductor version: Release (3.19)

This package contains: 1. A microarray gene expression dataset from a human breast cancer study. 2. A RNA-Seq gene expression dataset from a mouse study on IFNG knockout. 3. ID mapping tables between gene IDs and SBGN-ML file glyph IDs. 4. Percent of orthologs detected in other species of the genes in a pathway. Cutoffs of this percentage for defining if a pathway exists in another species. 5. XML text of SBGN-ML files for all pre-collected pathways.

Author: Xiaoxi Dong*, Kovidh Vegesna*, Weijun Luo

Maintainer: Weijun Luo <luo_weijun at yahoo.com>

Citation (from within R, enter citation("SBGNview.data")):

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("SBGNview.data")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("SBGNview.data")
Supporting Datasets for SBGNview Package HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews BreastCancerData, CancerData, ExperimentData, GEO, MicroarrayData, RNASeqData
Version 1.18.0
License AGPL-3
Depends R (>= 3.6)
Imports knitr, rmarkdown, bookdown
System Requirements
URL
See More
Suggests SummarizedExperiment
Linking To
Enhances
Depends On Me SBGNview
Imports Me
Suggests Me
Links To Me
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package SBGNview.data_1.18.0.tar.gz
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/SBGNview.data
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/SBGNview.data
Package Short Url https://bioconductor.org/packages/SBGNview.data/
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